SAN FRANCISCO -- Having given up at least 100 yards rushing in a game only once to a player not named Adrian Peterson, the Green Bay Packers felt confident about managing the 49ers running game.

Quarterback Colin Kaepernick changed all that Saturday night with an NFL record 181 yards rushing on 16 carries and doing it two different ways -- running the read option and breaking free from the pocket for scrambles on called pass plays.

The Packers, two years removed from their Super Bowl victory, were 45-31 losers at Candlestick Park after giving up 323 yards rushing on 43 carries.

Running back Frank Gore added 119 yards on 23 carries and a touchdown, operating as Mr. Inside to Kaepernick's Mr. Outside. Gore, with 112 yards rushing in the season opener at Green Bay, was the only runner other than Peterson to crack 100 yards on the Packers all season.

Kaepernick scored on runs of 20 and 56 yards, in addition to throwing touchdown passes of 12 and 20 yards to Michael Crabtree. Completing 17 of 31 passes for 263 yards -- his second pass of the game was intercepted and returned 52 yards for a TD by Sam Shields -- Kaepernick torched Green Bay for 444 yards of total offense.

Yet it was Kaepernick's ability to run that left the Packers shaking their heads in the losing locker room.

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"We expected them to try and get him out on the perimeter," strong safety Charles Woodson said. "But we didn't expect him to do what he did."

Green Bay coach Mike McCarthy said the Packers had prepared for Kaepernick's skill as a runner and at times employed a spy to keep him in check. Green Bay defenders, however, were clearly on their heels and intimidated after Kaepernick had broken free a few times.

"The scrambles, when you're able to get a good rush and then he's able to get out, those are just backbreakers -- especially when it's third down and you need to get off the field," inside linebacker Erik Walden said. "Give him credit. He made plays."

Said Woodson: "Well, you can't let him out of there, it seems. You get some rushes on the guy and he finds that hole, and when he takes off, he's out of there like 10 yards a pop it seems every time he does it."

In terms of defending the option, defensive tackle B.J. Raji said the 49ers executed the plays to near-perfection.

"On defense, everyone's got an assignment -- we know what it is," Raji said. "Obviously he made it very difficult for us tonight."

Woodson conceded Kaepernick's running of the option left the Packers confused.

"The one thing it kind of does, is it makes you a little bit indecisive," Woodson said. "You want to shoot in there, but he may hold the ball and take it outside. You go outside, and he might give it to the running back and take it up the middle.

"It's one of those things, it makes you play flat-footed a little bit."

The game shifted for good after the Packers had tied it 24-24 on a 31-yard Mason Crosby field goal in the third quarter, only to have the 49ers go 80 yards in three plays -- with Kaepernick racing around right end for 56 yards and a touchdown.

"We knew he was going to run the football," McCarthy said. "We knew he was a factor pulling the ball down in the passing game and running, and we did not take it away from him."

As dominant as Kaepernick was, Woodson looked at the 49ers and saw a superior team.

"They're a deep team, they're a big team, they're a fast team, they're well-coached," he said. "I look at us and maybe we've got to be bigger and faster."